Hi Gleb, If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
loadall *.pdb import psico.fitting extra_fit *, reference, method=tmalign, object=aln remove not (byres aln) https://pymolwiki.org/index.php/Psico Cheers, Thomas > On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> wrote: > > Dear Pymol Users! > > In my work dir I have 200 pdb files of GPCRs and one receptor > reference.pdb (it consist of only one GPCR monomer - seven > transmbembrane scaffold). > > I need to write a simple script which will do the following things: > > 1 - allign (in loop) each structure against reference.pdb using > "super" or "TMalign" (is better!) > > 2 - from each of the aligned pdbs, remove not superimposed regions > (assuming that each pdb has several chains, some insertions like > lyzocyme which were not aligned against reference), thus keeping only > seven-transmembrane scaffold present in reference.pdb. > > I thanks so much for the help! > > Gleb -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
